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Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes:

List of all members.


Class Summary

Synopsis

    $set_neighbour_nodes-\>fetch_input();
    $set_neighbour_nodes-\>run();
    $set_neighbour_nodes-\>write_output(); writes to database

Description

 

Definition at line 20 of file SetNeighbourNodes.pm.

Available Methods

public alignment_type ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public void deprecate ()
public DESTROY ()
public end ()
public void fetch_input ()
public fetch_trees ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public mlss_id ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public root_id ()
public run ()
public Arrayref runnable ()
public set_neighbour_nodes_for_internal_node ()
public set_of_species ()
public Array stack_trace ()
public String stack_trace_dump ()
public start ()
public step ()
public strict_hash_format ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::alignment_type ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::end ( )

Undocumented method

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public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for gerp from the database
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::fetch_trees ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::get_params ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::mlss_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::root_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::run ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::set_neighbour_nodes_for_internal_node ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::set_of_species ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::start ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetNeighbourNodes::step ( )

Undocumented method

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The documentation for this class was generated from the following file: